Cryptic genetic variation enhances primate L1 retrotransposon survival by enlarging the functional coiled coil sequence space of ORF1p

Accounting for continual evolution of deleterious L1 retrotransposon families, which can contain hundreds to thousands of members remains a major issue in mammalian biology. L1 activity generated upwards of 40% of some mammalian genomes, including humans where they remain active, causing genetic defects and rearrangements. L1 encodes a coiled coil-containing protein that is essential for retrotransposition, and the emergence of novel primate L1 families has been correlated with episodes of extensive amino acid substitutions in the coiled coil. These results were interpreted as an adaptive response to maintain L1 activity, however its mechanism remained unknown. Although an adventitious mutation can inactivate coiled coil function, its effect could be buffered by epistatic interactions within the coiled coil, made more likely if the family contains a diverse set of coiled coil sequences—collectively referred to as the coiled coil sequence space. Amino acid substitutions that do not affect coiled coil function (i.e., its phenotype) could be “hidden” from (not subject to) purifying selection. The accumulation of such substitutions, often referred to as cryptic genetic variation, has been documented in various proteins. Here we report that this phenomenon was in effect during the latest episode of primate coiled coil evolution, which occurred 30–10 MYA during the emergence of primate L1Pa7–L1Pa3 families. First, we experimentally demonstrated that while coiled coil function (measured by retrotransposition) can be eliminated by single epistatic mutations, it nonetheless can also withstand extensive amino acid substitutions. Second, principal component and cluster analysis showed that the coiled coil sequence space of each of the L1Pa7-3 families was notably increased by the presence of distinct, coexisting coiled coil sequences. Thus, sampling related networks of functional sequences rather than traversing discrete adaptive states characterized the persistence L1 activity during this evolutionary event.Author summary: Mammalian L1 retrotransposons replicate by copying their RNA into genomic DNA. Despite being deleterious, a single lineage of successive L1 families emerged in most mammalian genomes, each amplifying before undergoing extinction and replacement by another active family. During ~80 million years of primate evolution this process generated ~40% of the human genome where L1 remains active. Thus, accounting for the persistence of L1 is a major issue. Emergent L1 families are often associated with episodes of extensive amino substitutions in the L1 encoded ORF1p protein, which is required for L1 replication. These bore the signature of positive selection (more amino acid substitutions than expected by chance), which often indicates an adaptive change, implying an “arms race” between L1 and its host. Determing the contestants in this arms race would reveal a major aspect of L1/host interaction. But our findings now suggest an alternative evolutionary model. Most of the substitutions did not affect ORF1p function, and being “hidden” from selection their accumulation could increase sequence diversity (sequence space) of functional ORF1p, which we demonstrated by principal component analysis. The availability of multiple functional ORF1p sequences could buffer ORF1p activity from random inactivating mutations, an evolutionary strategy that could ensure L1 survival.